How the Red Sky Season could have been introduced
 

I actually thought the world was in a post apocalyptic state when I first saw the Red Sky episodes. But it made me think of this idea. What if they introduced it differently. Like this:

In Shredder Triumphant, Shredder still banishes them to Dimension X and Shredder and Krang continue to rule the city and other territories. The Turtles eventually do find a portal to get back to Earth, but by then they are too late. The city, and other parts of the planet are messed up and they are in a post apocalyptic world, thanks to the newly energized Technodrome. Since the world is in a post apocalyptic state, hence the reason why the red sky is present.

The show becomes more serious as Shredder and Krang basically took over the planet and the Turtles not only encounter old foes like Baxter, Leatherhead, and so forth, but of course battle all new ones like Megavolt, Lord Dregg, Chronos, Beserko Titanus and so forth. Some working for Krang and Shredder, and others are working for themselves.

Carter would still show up, but the Turtles would not mutate into hulks. Only Carter would do that since he was exposed to the newly changed mutagen. I always felt he should have been the only one to mutate, as it would set him apart from the others. Casey Jones, Mondo Gecko, Usagi, The Punk Frogs, and so forth would join in and help in the final battle. The city and others are overrun by foot soldiers and rock soldiers and they all fight for survival. Irma, Vernon and Burne would still be around and April as well, trying to help the Turtles.

They eventually infiltrate the Technodrome, defeat Granitor and Tragg and also Bebop and Rocksteady. Shredder eventually encounters Splinter and they have one final confrontation which eventually leads to Shredder's final defeat. They manage to blow up the Technodrome for good, but Krang emerges from the rubble and grows to the size of Godzilla like he did last time. The final battle would take place with the Turtles and their allies and they all fight a giant Krang, the final villain, to which eventually leads to Krang's defeat.

What would you think if the 1987 Turtles show ended this way?

I have my own ideas for how to work around all of that or allow what happened to happen and change it up from there. What you mention has been thinking of what might just be my favorite TMNT cover.

The mutation thing should have been a one episode thing or something. Also, why didn't this affect Splinter, Bebop and Rocksteady? That would have rasied the stakes having the B+R turn so dangerous even Shredder needed the Turtles to help him, and the Turtles not being safe in their own home as the new mutated Splinter attacks them.

There's a second crossover coming up with the 80s and Nick Turtles.

I think it would be pretty cool if some plot twist during that crossover resulted in the 80's dimension being severely polluted and permanently scarred into the form of the Red Sky look that starts from season 8.